Yuki Nishida

Manifest Contracts for Datatypes

We study algebraic data types in a manifest contract system, a software contract system where contract information occurs as refinement types. We first compare two simple approaches: refinements on type constructors and refinements on data constructors. For example, lists of positive integers can be described by {l:int list | for_all (lambda y. y > 0) l} in the former, whereas by a user-defined datatype pos_list with cons of type {x:int | x > 0} X pos_list -> pos_list in the latter. The two approaches are complementary: the former makes it easier for a programmer to write types and the latter enables more efficient contract checking. To take the best of both worlds, we propose (1) a syntactic translation from refinements on type constructors to equivalent refinements on data constructors and (2) dynamically checked casts between different but compatible datatypes such as int list and pos_list. We define a manifest contract calculus to formalize the semantics of the casts and prove that the translation is correct.

The pathophysiological significance of PPM1D and therapeutic targeting of PPM1D-mediated signaling by GSK2830371 in mantle cell lymphoma

PPM1D is a serine/threonine phosphatase that negatively regulates key DNA damage response proteins, such as p53, p38 MAPK, histone H2A.X, and ATM. We investigated the pathophysiological significance of PPM1D and its therapeutic targeting by the novel PPM1D inhibitor GSK2830371 in mantle cell lymphoma (MCL). Oncomine-based analyses indicated increased PPM1D mRNA levels in MCL cells compared with their normal counterpart cells. Higher PPM1D expression was associated with higher expression of the proliferation gene signature and poorer prognosis in patients. Eight MCL (three p53 wild-type and five mutant) cell lines were exposed to GSK2830371. GSK2830371 inhibited the cell growth, being prominent in p53 wild-type cells. GSK2830371 induced apoptosis in sensitive cells, as evidenced by induction of phosphatidylserine externalization and loss of mitochondrial membrane potential. p53 knockdown de-sensitized cell sensitivity. GSK2830371 increased the levels of total and Ser15-phosphorylated p53, and p53 targets p21 and PUMA. GSK2830371 and the MDM2 inhibitor Nutlin-3a acted synergistically in p53 wild-type cells. Interestingly, GSK2830371 sensitized MCL cells to bortezomib and doxorubicin in p53 wild-type and mutant cells; p38 signaling appeared to be involved in the GSK2830371/bortezomib lethality. PPM1D inhibition may represent a novel therapeutic strategy for MCL, which can be exploited in combination therapeutic strategies for MCL.

Sharper and Simpler Nonlinear Interpolants for Program Verification

Interpolation of jointly infeasible predicates plays important roles in various program verification techniques such as invariant synthesis and CEGAR. Intrigued by the recent result by Dai et al. that combines real algebraic geometry and SDP optimization in synthesis of polynomial interpolants, the current paper contributes its enhancement that yields sharper and simpler interpolants. The enhancement is made possible by: theoretical observations in real algebraic geometry; and our continued fraction-based algorithm that rounds off (potentially erroneous) numerical solutions of SDP solvers. Experiment results support our tools effectiveness; we also demonstrate the benefit of sharp and simple interpolants in program verification examples.

Nondeterministic Manifest Contracts

We study a manifest contract system---a typed calculus of higher-order contracts where contracts are tightly integrated into a refinement type system---for a functional language with nondeterministic choice. The extension is not trivial, especially in the presence of dependent function types, because a naive extension would lead to inconsistent type equivalence, which makes contract information in refinement types meaningless. To solve the problem, we propose a new kind of nondeterministic choice called coordinated choice, in which each occurrence of a choice operator is given a name and choices of the same name coordinately take the same branch. We introduce the notion of or-thant that helps both intuitive understanding and the development of formal semantics of the new choice. We formalize a manifest contract system λ H||Φ using the coordinated choice and show its basic properties of progress, type preservation, and contract satisfaction, the last of which states correctness of contracts in refinement types.

Targeting of BMI-1 expression by the novel small molecule PTC596 in mantle cell lymphoma

Despite the development of the novel Bruton tyrosine kinase inhibitor ibrutinib, mantle cell lymphoma (MCL) remains an incurable B-cell non-Hodgkin lymphoma. BMI-1 is required for the self-renewal and maintenance of MCL-initiating stem cells. Upregulation of BMI-1 has been reported in MCL patients, especially in those with refractory/relapsed disease. We studied the effects of a novel small-molecule selective inhibitor of BMI1 expression, PTC596, in MCL cells. Eight MCL cell lines and patient-derived samples were exposed to PTC596. PTC596 induced mitochondrial apoptosis, as evidenced by loss of mitochondrial membrane potential, caspase-3 cleavage, BAX activation, and phosphatidylserine externalization. There was a positive correlation between baseline BMI-1 protein levels and PTC596-induced apoptosis. p53 status did not affect sensitivity to PTC596. PTC596 effectively decreased BMI-1-expressing and tumor-initiating side population MCL cells (IC50: 138 nM) compared with ibrutinib, which modestly decreased side population cells. Interestingly, PTC596, reported to target cancer stem cells, decreased MCL-1 expression levels and antagonized ibrutinib-induced increase in MCL-1 expression, leading to synergistic apoptosis induction in MCL cells. There are currently no drugs that specifically target cancer stem cell fractions, and a reduction in BMI-1 protein by PTC596 may offer a novel therapeutic strategy for MCL.

Paraneoplastic Sarcoidosis in Multiple Myeloma

Sarcoidosis predominantly affects the lungs, intrathoracic lymph nodes, and eyes; it less frequently affects the musculoskeletal system. We herein report a case of paraneoplastic sarcoidosis in a patient presenting with multiple myeloma. The patient developed ocular sarcoidosis and showed an increased 18F-fluorodeoxyglucose uptake in the mediastinal lymph nodes and vertebral column. A lymph node specimen showed the histological features of sarcoidosis, while an examination of the vertebral tumor revealed myeloma. Although the simultaneous occurrence of sarcoidosis and myeloma is extremely rare, our case indicates the importance of exculing any underlying malignancies before establishing a diagnosis of skeletal sarcoidosis when bone lesions are observed at unusual sites.

Abstract 3730: The PPM1D inhibitor GSK2830371 has p53-dependent anti-lymphoma effects and enhances bortezomib-induced apoptosis in mantle cell lymphoma

p53 mutations are relatively rare (∼15%) in mantle cell lymphoma (MCL). Chemotherapeutic agents induce DNA damage, p53 phosphorylation and pro-apoptotic wild-type (WT) p53 signaling, resulting in lymphoma cell death. However, DNA damaging agents may have severe acute toxicities, accelerate clonal evolution and cause therapy-related neoplasms by adding new mutations to the original clones. PPM1D is a serine/threonine phosphatase that negatively regulates key DNA damage response proteins including p53, CHK2, Histone H2AX, and ATM. PPM1D has been thought to be an oncogenic protein. It has been reported that PPM1D is overexpressed or amplified in breast and ovarian cancers. GSK2830371 (GSK) is a PPM1D inhibitor, which binds to a flap subdomain that regulates enzymatic activity of PPM1D and substrate recognition (Nat Chem Biol 2014). Treatment of tumor cells with the inhibitor GSK has been found to increase phosphorylation of PPM1D substrates and cause growth inhibition in tumor cells harboring wild-type p53. We investigated the clinical significance of PPM1D and anti-lymphoma effects of GSK in MCL. The mRNA expression levels in patient samples were determined using Oncomine. Our gene expression analyses showed an increase in PPM1D mRNA expression in MCL samples versus normal naive B lymphocytes (P = 0.044) that are the normal counterparts of MCL. PPM1D mRNA levels were positively correlated with CCND1 (encoding Cyclin D1) mRNA levels (r = 0.33, P = 0.0014) and proliferation signature averages (r = 0.54, P Citation Format: Kensuke Kojima, Mariko Yoshimura, Aya Maeda, Hiroaki Kitamura, Yuki Nishida, Shinya Kimura. The PPM1D inhibitor GSK2830371 has p53-dependent anti-lymphoma effects and enhances bortezomib-induced apoptosis in mantle cell lymphoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3730.